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- PDB-7d0u: Structure of the CYP102A1 Haem Domain with N-enanthyl-L-prolyl-L-... -

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Basic information

Entry
Database: PDB / ID: 7d0u
TitleStructure of the CYP102A1 Haem Domain with N-enanthyl-L-prolyl-L-phenylalanine in complex with Ethylamine
ComponentsBifunctional cytochrome P450/NADPH--P450 reductase
KeywordsOXIDOREDUCTASE / Monooxygenase
Function / homology
Function and homology information


NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / aromatase activity / metabolic process / FMN binding / iron ion binding / heme binding / identical protein binding / cytoplasm
Similarity search - Function
Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding ...Bifunctional cytochrome P450/NADPH--cytochrome P450 reductase / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Flavoprotein-like superfamily / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
Chem-D0L / PROTOPORPHYRIN IX CONTAINING FE / ETHANAMINE / Bifunctional cytochrome P450/NADPH--P450 reductase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.68 Å
AuthorsStanfield, J.K. / Sugimoto, H. / Shoji, O.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR15P3 Japan
CitationJournal: To Be Published
Title: Structure of the CYP102A1 Haem Domain with N-enanthyl-L-prolyl-L-phenylalanine in complex with Ethylamine at 1.68 Angstrom Resolution
Authors: Shoji, O. / Stanfield, J.K.
History
DepositionSep 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional cytochrome P450/NADPH--P450 reductase
B: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,47417
Polymers104,6012
Non-polymers2,87315
Water10,124562
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A: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7839
Polymers52,3011
Non-polymers1,4838
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-21 kcal/mol
Surface area19040 Å2
MethodPISA
2
B: Bifunctional cytochrome P450/NADPH--P450 reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6918
Polymers52,3011
Non-polymers1,3907
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-21 kcal/mol
Surface area19140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.897, 128.581, 148.938
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Bifunctional cytochrome P450/NADPH--P450 reductase / Cytochrome P450(BM-3) / Cytochrome P450BM-3 / Fatty acid monooxygenase / Flavocytochrome P450 BM3


Mass: 52300.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: cyp102A1 / Production host: Escherichia coli (E. coli)
References: UniProt: P14779, unspecific monooxygenase, NADPH-hemoprotein reductase

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Non-polymers , 5 types, 577 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-D0L / (2S)-2-[[(2S)-1-heptylpyrrolidin-2-yl]carbonylamino]-3-phenyl-propanoic acid


Mass: 360.490 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H32N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NEH / ETHANAMINE / Ethylamine


Mass: 45.084 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H7N / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 562 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.37 %
Crystal growTemperature: 293 K / Method: batch mode
Details: PEG 8000, Magnesium Chloride, Tris-HCl, 0.5 % DMSO, 200 uM N-enanthyl-L-prolyl-L-phenylalanine, 0.5 mM Ethylamine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.68→48.66 Å / Num. obs: 249765 / % possible obs: 99.9 % / Redundancy: 6.965 % / Biso Wilson estimate: 33.367 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.189 / Rrim(I) all: 0.205 / Χ2: 0.839 / Net I/σ(I): 10.59 / Num. measured all: 1739738
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.68-1.786.4811.9581.0326065440403402180.5372.1399.5
1.78-1.97.2111.2541.9827401037998379970.8211.351100
1.9-2.057.3380.8123.8125938635349353490.9450.874100
2.05-2.257.2940.5726.8323747932556325560.9810.616100
2.25-2.527.2070.42610.6321181829390293900.990.459100
2.52-2.96.6650.29215.2517315525983259800.9910.317100
2.9-3.556.3720.1622.7413977821938219360.9970.175100
3.55-5.016.9180.07335.6511734216962169620.9990.078100
5.01-48.667.0510.04938.4266116938693770.9990.05299.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.47
Highest resolutionLowest resolution
Rotation46.31 Å2.08 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREP11.7.02phasing
REFMAC5.8.0266refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XA3

5xa3


Resolution: 1.68→48.66 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.456 / SU ML: 0.078 / SU R Cruickshank DPI: 0.0969 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.214 6500 5 %RANDOM
Rwork0.1857 ---
obs0.1872 123286 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.47 Å2 / Biso mean: 27.794 Å2 / Biso min: 14.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0 Å20 Å2
2--0.95 Å2-0 Å2
3----0.76 Å2
Refinement stepCycle: final / Resolution: 1.68→48.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7328 0 287 562 8177
Biso mean--31.8 33.84 -
Num. residues----908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0138038
X-RAY DIFFRACTIONr_bond_other_d0.0030.0177587
X-RAY DIFFRACTIONr_angle_refined_deg1.691.69610944
X-RAY DIFFRACTIONr_angle_other_deg1.4321.61617545
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7615958
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17823.46422
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13151396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4111541
X-RAY DIFFRACTIONr_chiral_restr0.0890.2983
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029199
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021834
LS refinement shellResolution: 1.68→1.722 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.388 478 -
Rwork0.358 8906 -
obs--99.12 %

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